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Bumbrah GS, Jain S, Fatima Z, Hameed S. Efficacy of LAMP assay for Mycobacterial spp. detection to prevent treatment delays and onset of drug resistance: a systematic review and meta-analysis. Drug Target Insights 2023; 17:78-89. [PMID: 37304408 PMCID: PMC10249090 DOI: 10.33393/dti.2023.2596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Background Tuberculosis (TB) remains a deadly disease affecting one-third population globally. Long turnaround time and poor sensitivity of the conventional diagnostics are the major impediments for faster diagnosis of Mycobacterial spp to prevent drug resistance. To overcome these issues, molecular diagnostics have been developed. They offer enhanced sensitivity but require sophisticated infrastructure, skilled manpower and remain expensive. Methods In that context, loop-mediated isothermal amplification (LAMP) assay, recommended by the WHO in 2016 for TB diagnosis, sounds as a promising alternative that facilitates visual read outs. Therefore, the aim of the present study is to conduct a meta-analysis to assess the diagnostic efficiency of LAMP for the detection of a panel of Mycobacterium spp. following PRISMA guidelines using scientific databases. From 1600 studies reported on the diagnosis of Mycobacterium spp., a selection of 30 articles were identified as eligible to meet the criteria of LAMP based diagnosis. Results It was found that most of the studies were conducted in high disease burden nations such as India, Thailand, and Japan with sputum as the most common specimen to be used for LAMP assay. Furthermore, IS6110 gene and fluorescence-based detections ranked as the most used target and method respectively. The accuracy and precision rates mostly varied between 79.2% to 99.3% and 73.9% to 100%, respectively. Lastly, a quality assessment based on QUADAS-2 of bias and applicability was conducted. Conclusion LAMP technology could be considered as a feasible alternative to current diagnostics considering high burden for rapid testing in low resource regions.
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Affiliation(s)
- Gurvinder Singh Bumbrah
- Department of Forensic Sciences, Amity School of Applied Sciences, Amity University Haryana, Gurugram, Manesar - India
| | - Sarika Jain
- Department of Mathematics, Amity School of Applied Sciences, Amity University Haryana, Gurugram, Manesar - India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar - India
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha - Saudi Arabia
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, Manesar - India
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2
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Rudeeaneksin J, Klayut W, Srisungngam S, Bunchoo S, Toonkomdang S, Wongchai T, Chuenchom N, Phetsuksiri B. Putative extensive and pre-extensive drug resistant-tuberculosis associated with unusual genotypes on the Thailand-Myanmar border. Rev Inst Med Trop Sao Paulo 2021; 63:e85. [PMID: 34878043 PMCID: PMC8660029 DOI: 10.1590/s1678-9946202163085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
Extensive drug-resistant tuberculosis (XDR-TB) is highly life threatening and its
diagnosis is usually difficult and time-consuming. Here we present the first two
cases of XDR and pre-XDR-TB diagnosed in 2018 on the Thailand-Myanmar border,
more specifically in Tak province. Rapid detection of XDR-TB was performed by
loop-mediated isothermal amplification (LAMP), Xpert MTB/RIF, and line probe
assays. Mutation analyses targeting rpoB,
katG, inhA, gyrA and
rrs genes showed an association with drug-resistant
phenotypes, except for rifampicin resistance. Spoligotyping revealed uncommon
Beijing and T2 genotypes and the analysis of M. tuberculosis
interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) showed
the presence of more polymorphisms. This report highlights the importance of the
early detection of drug-resistant tuberculosis by molecular tests followed by
phenotyping assays. Based on the up-to-date definition of XDR- and pre-XDR-TB,
the susceptibility testing for bedaquiline and linezolid is required and the two
reported cases may correspond to putative XDR-TB.
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Affiliation(s)
- Janisara Rudeeaneksin
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Wiphat Klayut
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sopa Srisungngam
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Supranee Bunchoo
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | | | | | | | - Benjawan Phetsuksiri
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand.,Ministry of Public Health, Medical Sciences Technical Office, Department of Medical Sciences, Nonthaburi, Thailand
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3
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Cao XJ, Li YP, Wang JY, Zhou J, Guo XG. MPT64 assays for the rapid detection of Mycobacterium tuberculosis. BMC Infect Dis 2021; 21:336. [PMID: 33838648 PMCID: PMC8035777 DOI: 10.1186/s12879-021-06022-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
Background Tuberculosis (TB) is a serious infectious disease caused by Mycobacterium tuberculosis (MTB). An estimated 1.7 billion people worldwide are infected with Mycobacterium tuberculosis (LTBI) during the incubation period without any obvious symptoms. Because of MTB’s high infection and mortality rates, there is an urgent need to develop a fast, portable, and sensitive diagnostic technology for its detection. Methods We included research from PubMed, Cochrane Library, Web of Science, and Embase and extracted the data. MetaDisc and STATA were used to build forest plots, Deek’s funnel plot, Fagan plot, and bivariate boxplot for analysis. Results Forty-six articles were analyzed, the results of which are as follows: sensitivity and specificity were 0.92 (0.91–0.93) and 0.95 (0.94–0.95) respectively. The NLR and PLR were 0.04 (95% CI 0.03–0.07) and 25.32 (95% CI 12.38–51.78) respectively. DOR was 639.60 (243.04–1683.18). The area under the SROC curve (AUC) was 0.99. Conclusions MPT64 exhibits good diagnostic efficiency for MTB. There is no obvious heterogeneity between the three commercial kits. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06022-w.
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Affiliation(s)
- Xun-Jie Cao
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Ya-Ping Li
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China.,Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Jia-Ying Wang
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Jie Zhou
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China. .,Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China. .,Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China. .,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
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4
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Phetsuksiri B, Klayut W, Rudeeaneksin J, Srisungngam S, Bunchoo S, Toonkomdang S, Wongchai T, Nakajima C, Suzuki Y. The performance of an in-house loop-mediated isothermal amplification for the rapid detection of Mycobacterium tuberculosis in sputum samples in comparison with Xpert MTB/RIF, microscopy and culture. Rev Inst Med Trop Sao Paulo 2020; 62:e36. [PMID: 32520211 PMCID: PMC7274762 DOI: 10.1590/s1678-9946202062036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022] Open
Abstract
Simple, low-cost and effective diagnostic tests for tuberculosis (TB) are needed especially in TB-high burden settings. The present study evaluated the performance of an in-house loop-mediated isothermal amplification (LAMP) for diagnosing TB by comparing it to Xpert MTB/RIF, microscopy and culture. In Thailand, a total of 204 excess sputum samples volume after the processing of cultures were used for Mycobacterium tuberculosis (MTB) detection by Xpert MTB/RIF and LAMP. Based on culture results as the gold standard, the overall sensitivity of LAMP and Xpert MTB/RIF were 82.1% (126/153; 95% confidential interval [CI]: 75.4-88.98%) and 86.9 % (133/153; 95% CI: 80.5-90.8%) respectively, and the specificity of both tests was 100% (51/51; 95% CI: 93.0-100.0%). In comparison with Xpert MTB/RIF, the sensitivity and specificity of LAMP were 94.7% (126/133; 95% CI: 89.5-97.9%), and 100.0% (73/73; 95% CI: 94.9-100.0%), respectively. The average threshold cycle (Ct) of Xpert MTB/RIF detection for positive and negative LAMP results was statistically different, of 18.4 and 27.0, respectively (p < 0.05). In comparison with the acid-fast staining technique, and analyzing LAMP and Xpert MTB/RIF in smear-negative/culture-positive specimens, there was an increase of the detection rate by 47.7% (21/44) and 54.6% (24/44). The diagnostic sensitivity and specificity of LAMP appeared to be comparable to those of Xpert MTB/RIF. We claim that this LAMP has potential to provide a sensitive diagnostic test for the rapid TB diagnosis. It allowed a fast detection of MTB before the cultures and it could be used in resource-limited laboratory settings.
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Affiliation(s)
- Benjawan Phetsuksiri
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Wiphat Klayut
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Janisara Rudeeaneksin
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Sopa Srisungngam
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | - Supranee Bunchoo
- Ministry of Public Health, National Institute of Health, Department of Medical Sciences, Nonthaburi, Thailand
| | | | - Thanee Wongchai
- Mae Sot Hospital, Department of Medical Technology, Tak, Thailand
| | - Chie Nakajima
- Hokkaido University, Research Center for Zoonosis Control, Division of Bioresources, Sapporo, Japan.,Hokkaido University, Global Institution for Collaborative Research and Education, Global Station for Zoonosis Control, Sapporo, Japan
| | - Yasuhiko Suzuki
- Hokkaido University, Research Center for Zoonosis Control, Division of Bioresources, Sapporo, Japan.,Hokkaido University, Global Institution for Collaborative Research and Education, Global Station for Zoonosis Control, Sapporo, Japan
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Phetsuksiri B, Rudeeaneksin J, Srisungngam S, Bunchoo S, Klayut W, Nakajima C, Hamada S, Suzuki Y. Comparison of Loop-Mediated Isothermal Amplification, Microscopy, Culture, and PCR for Diagnosis of Pulmonary Tuberculosis. Jpn J Infect Dis 2020; 73:272-277. [PMID: 32115540 DOI: 10.7883/yoken.jjid.2019.335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The diagnosis of tuberculosis (TB) in endemic countries is challenging due to high caseloads and limited resources. A simple and cost-effective diagnostic test for the rapid detection of Mycobacterium tuberculosis (M. tuberculosis) in clinical specimens is crucially needed. We evaluated the performance of an in-house assay based on loop-mediated isothermal amplification (LAMP) targeting the M. tuberculosis 16S ribosomal RNA (rRNA) gene for the diagnosis of TB in Thailand. A total of 252 sputum samples from suspected cases of pulmonary TB were analyzed. The sensitivity of LAMP was 99.04% (103/104; 95% confidence interval [CI]: 94.76-9.98%) and 72.73% (16/22; 95% CI: 49.78-89.27%) for smear-positive and smear-negative samples with TB-culture positivity, respectively. LAMP detected 20.69% (24/116) of TB culture negative samples but all those were positive by conventional polymerase chain reaction (PCR). The sensitivity of LAMP was higher than that of sputum microscopy while the performance of LAMP was similar to PCR. None of the samples positive for non-tuberculous mycobacteria by culture and PCR were positive by LAMP. Compared to TB culture, the positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient of LAMP were 83.22%, 88.33%, and 0.75 respectively. Based on the diagnostic performance, we propose that LAMP would be suitable as a potential diagnostic test for rapid TB diagnosis in resource-limited laboratory settings.
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Affiliation(s)
- Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Janisara Rudeeaneksin
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Sopa Srisungngam
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Supranee Bunchoo
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Wiphat Klayut
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Japan
| | - Shigeyuki Hamada
- Section of Bacterial Infections, Research Collaboration Center for Emerging and Re-emerging Infectious Diseases, Thailand.,Research Institute for Microbial Diseases, Osaka University, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Japan
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